Chapter 18:
The Genetics of
Viruses and
Bacteria
What is Microbiology?
 Microbiology is the science that studies
microorganisms
 Microorganisms, roughly, are those living things
that are too small to be seen with the naked eye
 Microorganisms cannot be distinguished
phylogenetically from “Macroorganisms”, e.g.,
includes fungi as well as bacteria, etc. (that is,
they are not, as a whole, a closely related group
of organisms)
 Microbiology is more a collection of techniques:
Aseptic technique, Pure culture technique,
Microscopic observation of whole organisms, etc.
 A microbiologist usually first isolates a specific
microorganism from a population and then
cultures it
Importance of Microbes
 Microbes are producers—they provide energy to
ecosystems
 Microbes are fixers—they make nutrients available
from inorganic sources, e.g., nitrogen
 Microbes are decomposers—they free up nutrients
from no longer living sources
 Microbes form symbioses (such as mycorrhizal fungi
associated with plant roots—though these are
somewhat macroscopic; also the bacteria found in
legume root nodules, etc.)
 Microbes serve as endosymbionts (e.g., chloroplasts
and mitochondria)
 Microbes make fermentation products (ethanol!), food
(beer! Cheese! Yogurt! Half-sour pickles!), Biotech
products (e.g., recombinant insulin), etc.
 Germ theory of disease; Normal flora
Relative Microbe Sizes
Examples of Types of Viruses
What is a Virus?
 Viruses consist of protein capsids and nucleic
acid (DNA or RNA) plus some viruses (virions)
have a lipid envelope (enveloped viruses)
 Viruses are… “...infectious agents of small size
and simple composition that can multiply only in
living cells of animals, plants and bacteria [plus
fungi & protozoa].
 Viruses are obligate parasites that are
metabolically inert when they are outside their
hosts. They all rely, to varying extents, on the
metabolic processes of their hosts to reproduce
themselves.
 The viral diseases we see are due to the effects
of this interaction between the virus and its host
cell (and/or the host’s response to this
interaction).” Encyclopedia Britannica
Virus (Virion Particle)
The Virion is what defines a virus as a virus
A Virion is the extracellular state of a virus
The job of Virions is to find new cells to infect
As such, Virions are a durable state that is
“designed” to attach to susceptible cells
The Virion is then responsible for
translocation of the virus genome into the cell
The Virion consists of a DNA (or RNA)
genome surrounded by Protein that, in turn,
may be surrounded by a Lipid Bilayer
The Protein layer is called a Capsid
The Lipid Bilayer is called an Envelope
Steps of Virus Replication
1. Adsorption (attachment)
2. Penetration (nucleic-acid release)
3. Synthesis (of RNA and proteins, as
well as DNA if DNA genome)
4. Maturation (assembly of virion)
5. Release (lysis or chronic release, e.g.,
budding, with the latter coinciding with
release for various enveloped viruses)
Caveat: It is important to realize that variation among
viruses is between virus strains/species; any one kind of
virus cannot replicate in multiple ways, have more than one
virion morphology, or vary in genome type, etc.
DNA Virus Life Cycle
Lysis
Bacteriophage Lytic Cycle
Lysis
Lysogenic Cycle (Temperate
Phage)
Lysis
Only
temperate
phage are
able to
display
lysogeny
Enveloped RNA Virus
An
example of
an animal
virus
Budding
Acquisition of
plasma membrane
as envelope
HIV Life Cycle
Budding
HIV Life Cycle
Bacteria Sex
 Viruses move genetic material from cell to
cell
 Mostly this material is their own genomes,
i.e., genes that collectively code for the
production of new viruses
 Bacteria DNA also can move from cell to cell
 Once received by a cell, this DNA may be
incorporated into the bacterial genome via
recombination
 This idea of DNA sourced from different
parents recombining into a single
chromosome is equivalent to eukaryotic sex
(i.e., fertilization followed by recombination)
 Transformation, Transduction, Conjugation
Why study bacterial genetics?
• Its an easy place to start
– history
– we know more about it
• systems better understood
– simpler genome
– good model for control of genes
• build concepts from there to eukaryotes
– bacterial genetic systems are exploited in
biotechnology
Bacteria
• Bacteria review
– one-celled organisms
– prokaryotes
– reproduce by binary fission
– rapid growth
• generation every ~20 minutes
• 108 (100 million) colony overnight!
– dominant form of life on Earth
– incredibly diverse
Bacterial genome
• Single circular chromosome
– haploid
– naked DNA
• no histone proteins
– ~4 million base pairs
• ~4300 genes
• 1/1000 DNA in eukaryote
Intro to Bacteria video
No nucleus!
• No nuclear membrane
– chromosome in cytoplasm
– transcription & translation are coupled
together
• no processing of mRNA
– no introns
– but Central Dogma
still applies
• use same
genetic code
Binary fission
• Replication of bacterial
chromosome
• Asexual reproduction
– offspring genetically
identical to parent
– where does variation
come from?
Variation in bacteria
• Sources of variation
– spontaneous mutation
– transformation
• plasmids
• DNA fragments
– transduction
– conjugation
– transposons
bacteria shedding DNA
Transformation
Transformation: DNA picked up
directly from the medium and
recombined into the genome
Competent cell:
capable of
picking up DNA
Generalized Transduction
Plasmids
Conjugation
Moves plasmid
more so than
chromosomal
DNA
Bacterial Genetics
Regulation of Gene Expression
Bacterial metabolism
• Bacteria need to respond quickly to
changes in their environment
– if have enough of a product,
need to stop production
• why? waste of energy to produce more
• how? stop production of synthesis enzymes
– if find new food/energy source,
need to utilize it quickly
• why? metabolism, growth, reproduction
• how? start production of digestive enzymes
Regulation of Metabolism
e.g.,
transcription
Reminder: Regulation of
metabolism
• Feedback inhibition
– product acts
as an allosteric
inhibitor of
1st enzyme in
tryptophan pathway
-
= inhibition
Another way to Regulate
metabolism
• Gene regulation
– block transcription of
genes for all
enzymes in
tryptophan pathway
• saves energy by
not wasting it on
unnecessary protein
synthesis
-
= inhibition
Gene regulation in bacteria
• Control of gene expression enables
individual bacteria to adjust their
metabolism to environmental change
• Cells vary amount of specific enzymes
by regulating gene transcription
– turn genes on or turn genes off
• ex. if you have enough tryptophan in your cell
then you don’t need to make enzymes used to
build tryptophan
– waste of energy
– turn off genes which codes for enzymes
Control of Gene Expression
 Operons- sequence of DNA that directs particular
biosynthetic pathways
 4 Major Components of an operon
Regulatory gene- produces a repressor protein
that prevents gene expression by blocking DNA
polymerase
Promotor region- sequence of DNA where RNA
Polymerase attaches for transcription
Operator region- can block action of RNA
Polymerase if region is occupied by repressor
protein
Structural gene- contain DNA sequence that
code for several related enzymes that direct
production of an end product.
Control of Gene Expression
 It makes energetic sense to make or use proteins
responsible for certain metabolic processes only
when those processes are needed.
 Trp Operon- enzymes make needed tryptophan
Repressor inactivated in response to presence of
tryptophan
Tryptophan acts as Corepressor
“Repressable enzymes”- Usually turned on and
has to be turned off.
 Lac Operon
Controls breakdown of lactose
Lactose presence needed to turn on Operon
“inducible enzymes”- Usually turned off and
needs to be turned on.
So how can genes be turned
off?
• First step in protein production?
– transcription
– stop RNA polymerase!
• Repressor protein
– binds to DNA near promoter region blocking
RNA polymerase
• binds to operator site on DNA
• blocks transcription
Genes grouped together
• Operon
– genes grouped together with related functions
• ex. enzymes in a synthesis pathway
– promoter = RNA polymerase binding site
• single promoter controls transcription of all genes in operon
• transcribed as 1 unit & a single mRNA is made
– operator = DNA binding site of regulator protein
Trp Operon (low trp densities)
Recall that the promoter
is the site of RNA
polymerase binding
Don’t worry about the names of
these genes and products
Trp Operon (higher trp densities)
Corepression
Negative
regulation
Equilibrium: Likelihood of
being in bound state
depends on trp density
Repressor protein model
Operon:
operator, promoter & genes they control
serve as a model for gene regulation
RNA
polymerase
RNA
TATA repressor
polymerase
promoter
operator
gene1
gene2
gene3
gene4
DNA
Repressor protein turns off gene by
blocking RNA polymerase binding site.
repressor
repressor protein
Repressible operon: tryptophan
Synthesis pathway model
RNA
polymerase
When excess tryptophan is present,
binds to tryp repressor protein &
triggers repressor to bind to DNA
RNA
TATA repressor
polymerase
gene1
– blocks (represses) transcription
gene2
gene3
gene4
repressor
promoter
DNA
repressor protein
operator
tryptophan
repressor
tryptophan – repressor protein
complex
conformational change in
repressor protein!
Tryptophan operon
What happens when tryptophan is present?
Don’t need to make tryptophan-building
enzymes
Tryptophan binds allosterically to regulatory protein
Inducible operon: lactose
Digestive pathway model
RNA
polymerase
When lactose is present, binds to
lac repressor protein & triggers
repressor to release DNA
RNA
TATA repressor
polymerase
gene1
– induces transcription
gene2
gene3
repressor
promoter
gene4
DNA
repressor protein
operator
lactose
repressor
lactose – repressor protein
complex
conformational change in
repressor protein!
Lactose operon
What happens when lactose is present?
Need to make lactose-digesting enzymes
Lactose binds allosterically to regulatory protein